cmip package

Submodules

cmip.cmip_titration module

Module containing the Titration class and the command line interface.

class cmip.cmip_titration.CmipTitration(input_pdb_path: str, output_pdb_path: str, input_vdw_params_path: str | None = None, input_params_path: str | None = None, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_cmip Titration
Wrapper class for the CMIP titration module.
The CMIP titration module. CMIP titration module adds water molecules, positive ions (Na+) and negative ions (Cl-) in the energetically most favorable structure locations.
Parameters:
  • input_pdb_path (str) – Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) –

    Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_vdw_params_path (str) (Optional) – Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used (“$CONDA_PREFIX/share/cmip/dat/vdwprm”). File type: input. Accepted formats: txt (edam:format_2330).

  • input_params_path (str) (Optional) – Path to the CMIP input parameters file. File type: input. Accepted formats: txt (edam:format_2330).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • params (dict) - ({}) CMIP options specification.

    • energy_cutoff (float) - (9999.9) Energy cutoff, extremely hight value to enable the addition of all the ions and waters before reaching the cutoff.

    • num_wats (int) - (10) Number of water molecules to be added.

    • neutral (bool) - (False) Neutralize the charge of the system. If selected num_positive_ions and num_negative_ions values will not be taken into account.

    • num_positive_ions (int) - (10) Number of positive ions to be added (Tipatom IP=Na+).

    • num_negative_ions (int) - (10) Number of negative ions to be added (Tipatom IM=Cl-).

    • binary_path (str) - (“titration”) Path to the CMIP Titration executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Path to the binary executable of your container.

    • container_image (str) - (“cmip/cmip:latest”) Container Image identifier.

    • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

    • container_working_dir (str) - (None) Path to the internal CWD in the container.

    • container_user_id (str) - (None) User number id to be mapped inside the container.

    • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_cmip.cmip.titration import titration
prop = { 'binary_path': 'titration' }
titration(input_pdb_path='/path/to/myStructure.pdb',
          output_pdb_path='/path/to/newStructure.pdb',
          properties=prop)
Info:
launch() int[source]

Execute the Titration object.

cmip.cmip_titration.cmip_titration(input_pdb_path: str, output_pdb_path: str, input_vdw_params_path: str | None = None, input_params_path: str | None = None, properties: dict | None = None, **kwargs) int[source]

Create Titration class and execute the launch() method.

cmip.cmip_titration.main()[source]

cmip.cmip_run module

Module containing the Cmip class and the command line interface.

class cmip.cmip_run.CmipRun(input_pdb_path: str, input_probe_pdb_path: str | None = None, output_pdb_path: str | None = None, output_grd_path: str | None = None, output_cube_path: str | None = None, output_rst_path: str | None = None, input_rst_path: str | None = None, output_byat_path: str | None = None, output_log_path: str | None = None, input_vdw_params_path: str | None = None, input_params_path: str | None = None, output_json_box_path: str | None = None, output_json_external_box_path: str | None = None, input_json_box_path: str | None = None, input_json_external_box_path: str | None = None, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_cmip Titration
Wrapper class for the CMIP cmip module.
The CMIP cmip module. CMIP cmip module compute classical molecular interaction potentials.
Parameters:
  • input_pdb_path (str) –

    Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_probe_pdb_path (str) (Optional) – Path to the input probe file in PDB format. File type: input. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) (Optional) –

    Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_grd_path (str) (Optional) – Path to the output grid file in GRD format. File type: output. Accepted formats: grd (edam:format_2330).

  • output_cube_path (str) (Optional) – Path to the output grid file in cube format. File type: output. Accepted formats: cube (edam:format_2330).

  • output_rst_path (str) (Optional) – Path to the output restart file. File type: output. Accepted formats: txt (edam:format_2330).

  • input_rst_path (str) (Optional) – Path to the input restart file. File type: output. Accepted formats: txt (edam:format_2330).

  • output_byat_path (str) (Optional) – Path to the output atom by atom energy file. File type: output. Accepted formats: txt (edam:format_2330), out (edam:format_2330).

  • output_log_path (str) (Optional) –

    Path to the output CMIP log file LOG. File type: output. Sample file. Accepted formats: log (edam:format_2330).

  • input_vdw_params_path (str) (Optional) – Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used (“$CONDA_PREFIX/share/cmip/dat/vdwprm”). File type: input. Accepted formats: txt (edam:format_2330).

  • input_params_path (str) (Optional) – Path to the CMIP input parameters file. File type: input. Accepted formats: txt (edam:format_2330).

  • output_json_box_path (str) (Optional) –

    Path to the output CMIP box in JSON format. File type: output. Sample file. Accepted formats: json (edam:format_3464).

  • output_json_external_box_path (str) (Optional) –

    Path to the output external CMIP box in JSON format. File type: output. Sample file. Accepted formats: json (edam:format_3464).

  • input_json_box_path (str) (Optional) –

    Path to the input CMIP box in JSON format. File type: input. Sample file. Accepted formats: json (edam:format_3464).

  • input_json_external_box_path (str) (Optional) –

    Path to the input CMIP box in JSON format. File type: input. Sample file. Accepted formats: json (edam:format_3464).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • execution_type (str) - (“mip_pos”) Default options for the params file, each one creates a different params file. Values: check_only (Dry Run of CMIP), mip_pos (MIP O+ Mehler Solmajer dielectric), mip_neg (MIP O- Mehler Solmajer dielectric), mip_neu (MIP Oxygen Mehler Solmajer dielectric), solvation (Solvation & MEP), pb_interaction_energy (Docking Interaction energy calculation. PB electrostatics), docking (Docking Mehler Solmajer dielectric), docking_rst (Docking from restart file).

    • params (dict) - ({}) CMIP options specification.

    • binary_path (str) - (“cmip”) Path to the CMIP cmip executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Path to the binary executable of your container.

    • container_image (str) - (“cmip/cmip:latest”) Container Image identifier.

    • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

    • container_working_dir (str) - (None) Path to the internal CWD in the container.

    • container_user_id (str) - (None) User number id to be mapped inside the container.

    • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_cmip.cmip.cmip import cmip
prop = { 'binary_path': 'cmip' }
cmip(input_pdb_path='/path/to/myStructure.pdb',
          output_pdb_path='/path/to/newStructure.pdb',
          output_log_path='/path/to/newStructureLog.log',
          properties=prop)
Info:
launch() int[source]

Execute the Cmip object.

cmip.cmip_run.cmip_run(input_pdb_path: str, input_probe_pdb_path: str | None = None, output_pdb_path: str | None = None, output_grd_path: str | None = None, output_cube_path: str | None = None, output_rst_path: str | None = None, output_byat_path: str | None = None, output_log_path: str | None = None, input_vdw_params_path: str | None = None, input_params_path: str | None = None, output_json_box_path: str | None = None, output_json_external_box_path: str | None = None, input_json_box_path: str | None = None, input_json_external_box_path: str | None = None, properties: dict | None = None, **kwargs) int[source]

Create Cmip class and execute the launch() method.

cmip.cmip_run.main()[source]

cmip.cmip_prepare_structure module

Module containing the PrepareStructure class and the command line interface.

class cmip.cmip_prepare_structure.CmipPrepareStructure(input_pdb_path: str, output_cmip_pdb_path: str, input_topology_path: str | None = None, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_cmip PrepareStructure
Generate a CMIP suitable PDB input.
Generate a CMIP suitable PDB input from a common PDB file or a Topology + PDB file.
Parameters:
  • input_pdb_path (str) –

    Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_topology_path (str) (Optional) –

    Path to the input topology path. File type: input. Sample file. Accepted formats: zip (edam:format_3987), top (edam:format_3880), psf (edam:format_3882), prmtop (edam:format_3881).

  • output_cmip_pdb_path (str) –

    Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Path to the binary executable of your container.

    • container_image (str) - (“cmip/cmip:latest”) Container Image identifier.

    • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

    • container_working_dir (str) - (None) Path to the internal CWD in the container.

    • container_user_id (str) - (None) User number id to be mapped inside the container.

    • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_cmip.cmip.prepare_structure import prepare_structure
prop = { }
prepare_structure(input_pdb_path='/path/to/myStructure.pdb',
                  output_cmip_pdb_path='/path/to/newStructure.pdb',
                  properties=prop)
Info:
launch() int[source]

Execute the Cmip object.

cmip.cmip_prepare_structure.cmip_prepare_structure(input_pdb_path: str, output_cmip_pdb_path: str, input_topology_path: str | None = None, properties: dict | None = None, **kwargs) int[source]

Create Cmip class and execute the launch() method.

cmip.cmip_prepare_structure.main()[source]

cmip.cmip_prepare_pdb module

Module containing the PreparePDB class and the command line interface.

class cmip.cmip_prepare_pdb.CmipPreparePDB(input_pdb_path: str, output_cmip_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_cmip CmipPreparePDB
Class to add CMIP charges and atom types.
Add CMIP charges and atom types to a PDB structure using biobb_structure_checking.
Parameters:
  • input_pdb_path (str) –

    Input PDB file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_cmip_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • remove_water (bool) - (True) Remove Water molecules.

    • add_hydrogen (bool) - (True) Add Hydrogen atoms to the structure.

    • keep_hydrogen (bool) - (False) If add_hydrogen is True. All hydrogen atoms will be removed before adding the new ones unless this option is set True.

    • fix_sidechains (bool) - (True) Complete side chains (heavy atoms, protein only).

    • fix_backbone_atoms (bool) - (True) Add missing O, OXT backbone atoms.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_cmip.cmip.cmip_prepare_pdb import cmip_prepare_pdb
prop = { 'restart': False }
cmip_prepare_pdb(input_pdb_path='/path/to/myStructure.pdb',
            output_cmip_pdb_path='/path/to/newStructure.pdb',
            properties=prop)
Info:
launch() int[source]

Execute the PreparePDB object.

cmip.cmip_prepare_pdb.cmip_prepare_pdb(input_pdb_path: str, output_cmip_pdb_path: str, properties: dict | None = None, **kwargs) int[source]

Create PreparePDB class and execute the launch() method.

cmip.cmip_prepare_pdb.main()[source]

cmip.cmip_ignore_residues module

Module containing the IgnoreResidues class and the command line interface.

class cmip.cmip_ignore_residues.CmipIgnoreResidues(input_cmip_pdb_path: str, output_cmip_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_cmip CmipIgnoreResidues
Class to ignore residues in CMIP potential calculations.
Mark residues which will be ignored in the CMIP potential calculations except for dielectric definition.
Parameters:
  • input_cmip_pdb_path (str) –

    Input PDB file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_cmip_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • residue_list (str) - (None) Residue list in the format “Chain:Resnum” (no spaces between the elements) separated by commas. If no chain is provided all the residues in the pdb file will be market. ie: “A:3”.

    • ignore_all (bool) - (False) Mark all the residues in the PDB file.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_cmip.cmip.cmip_ignore_residues import cmip_ignore_residues
prop = { 'residue_list': "A:3" }
cmip_ignore_residues(input_cmip_pdb_path='/path/to/myStructure.pdb',
                output_cmip_pdb_path='/path/to/newStructure.pdb',
                properties=prop)
Info:
launch() int[source]

Execute the IgnoreResidues object.

cmip.cmip_ignore_residues.cmip_ignore_residues(input_cmip_pdb_path: str, output_cmip_pdb_path: str, properties: dict | None = None, **kwargs) int[source]

Create IgnoreResidues class and execute the launch() method.

cmip.cmip_ignore_residues.main()[source]